CLC Genomics Server
The CLC Genomics Server is shipped with the tools listed below, which can be started from CLC Genomics Workbench and CLC Server Command Line Tools. A subset can be launched using the CLC Main Workbench. Please refer to the CLC Genomics Workbench manual for details about the tools listed. Import and export tools are not listed explicitly here, but import and export of many sequence related formats as well as other formats is supported.
- Import
- Export
- Search for Reads in SRA
- Classical Sequence Analysis
- Create Pairwise Comparison
- Create Alignment
- K-mer Based Tree Construction
- Create Tree
- Model Testing
- Maximum Likelihood Phylogeny
- Annotate with GFF/GTF/GVF files
- Extract Sequences
- Create Motif List from Sequences
- Motif Search
- Translate to Protein
- Convert DNA to RNA
- Convert RNA to DNA
- Reverse Complement Sequence
- Find Open Reading Frames
- Download Pfam Database
- Pfam Domain Search
- Find and Model Structure
- Proteolytic Cleavage
- Molecular Biology Tools
- Trim Sequences
- Assemble Sequences
- Assemble Sequences to Reference
- Secondary Peak Calling
- Find Binding Sites and Create Fragments
- Add attB Sites
- Create Entry clone (BP)
- Create Expression clone (LR)
- Restriction Site Analysis
- BLAST
- BLAST
- BLAST at NCBI
- Download BLAST Databases
- Create BLAST Database
- Prepare Sequencing Data
- QC for Sequencing Reads
- Trim Reads
- Demultiplex Reads
- Quality Control
- QC for Targeted Sequencing
- Target Region Coverage Analysis
- QC for Read Mapping
- Whole Genome Coverage Analysis
- Resequencing Analysis
- Map Reads to Reference
- Map Long Reads to Reference
- Local Realignment
- Merge Read Mappings
- Remove Duplicate Mapped Reads
- Extract Consensus Sequence
- Create Consensus Sequences from Variants
- Basic Variant Detection
- Fixed Ploidy Variant Detection
- Low Frequency Variant Detection
- InDels and Structural Variants
- Structural Variant Caller for Long Reads
- Identify Known Mutations from Mappings
- Copy Number Variant Detection (Targeted)
- Detect Fusion Genes from DNA
- Identify Enriched Variants in Case vs Control Samples
- Identify Shared Variants
- Trio Analysis
- Annotate from Known Variants
- Annotate with Conservation Scores
- Annotate with Flanking Sequences
- Annotate with Repeat and Homopolymer Information
- Filter against Known Variants
- Filter Homozygous Reference Variants
- Remove Variants Present in Control Reads
- Create Variant Track Statistics Report
- Amino Acid Changes
- Predict Splice Site Effect
- GO Enrichment Analysis
- Download 3D Protein Structure Database
- Link Variants to 3D Protein Structure
- RNA-Seq and Small RNA Analysis
- Create Expression Browser
- Quantify miRNA
- Annotate with RNAcentral Accession Numbers
- Create Combined miRNA Report
- Extract IsomiR Counts
- PCA for RNA-Seq
- Create Sample Level Heat Map for RNA-Seq
- Create Feature Level Heat Map for RNA-Seq
- Create K-medoids Clustering for RNA-Seq
- RNA-Seq Analysis
- RNA-Seq Analysis for Long Reads
- Detect and Refine Fusion Genes
- Import Expression Data
- Differential Expression in Two Groups
- Differential Expression for RNA-Seq
- Create Venn Diagram for RNA-Seq
- Gene Set Test
- Create Expression Browser
- Microarray Analysis
- Create Box Plot
- Principal Component Analysis
- Proportion-based Statistical Analysis
- Gaussian Statistical Analysis
- Create MA Plot
- Create Scatter Plot
- Create Histogram
- Epigenomics Analysis
- Histone ChiP-Seq
- Transcription Factor ChIP-Seq
- Map Bisulfite Reads to Reference
- Call Methylation Levels
- Create RRBS-fragment Track
- Learn Peak Shape Filter
- Apply Peak Shape Filter
- Score Regions
- De Novo Sequencing
- De Novo Assembly
- Map Reads to Contigs
- De Novo Assemble Long Reads
- Polish Contigs with Reads
- Utility Tools
- Extract Annotated Regions
- Extract Reads
- Filter Based on Name
- Filter Based on Overlap
- Filter on Custom Criteria
- Rename Elements
- Rename Sequences in Lists
- Combine Reports
- Create Report from Table
- Create Sample Report
- Modify Report Type
- Create Sequence List
- Download Taxonomy
- Merge Overlapping Pairs
- Split Sequence List
- Subsample Sequence List
- Update Sequence Attributes
- Create Track List
- Convert to Tracks
- Convert from Tracks
- Create GC Content Graph
- Create Mapping Graph
- Identify Graph Threshold Areas
- Merge Annotation Tracks
- Merge Variant Tracks
- Annotate with Exon Numbers
- Annotate with Nearby Information
- Annotate with Overlap Information
- Collapse Overlapping Annotations
- Remove Information from Track
- Resize Annotations
The functionality of the CLC Genomics Server can be extended by installing Server plugins.
Latest improvements
CLC Genomics Server is under constant development and improvement. A detailed list of new features, improvements, bugfixes, and changes for the current version of CLC Genomics Server can be found at: